The Killzone Experiment
by imeanwaitwhat
Summary: Something during Thomas' surgery went horribly wrong. His memory is swiped, but his brain is far more damaged than they'd expected. Despite the fact that many disagree, they decide to keep Thomas out of the maze. What they don't know is that Thomas is regaining his memory, and fast. About his past, about WICKED and the killzone experiments. Who's side will he choose?
1. Prologue

**Disclaimer: **I do not own The Maze Runner trilogy or any of its characters. The plot, however, is mine.

* * *

**Full summary: **Something during Thomas' surgery went horribly wrong. His memories are swiped, but his brain is far more damaged than they'd expected. Despite the fact that many disagree, they decide to keep Thomas out of the Maze and away from Teresa. What they don't know, is that Thomas is regaining his memory faster than they ever could have imagined. About his past, about WICKED and the killzone experiments. It's only a matter of time before he remembers it all. All that he's done and has been done to him. Will he side with WICKED, the group that's supposedly doing everything for a greater good, or with the Gladers, who don't even know about his existence?

* * *

_**Prologue**_

* * *

It was the silent sound of someone desperately trying to catch her breath that finally drove Thomas frustrated. He'd laid there for what seemed like hours, unable to place the noise. Now he remembered. Someone was crying. He wasn't sure how he knew it was a girl, but he did. Every now and then she'd let out a small whimper. By the sound of it he guessed her at around the same age as him. That made him pause for a moment. How old was he? He didn't know. He heard the sound of a door opening.

''Come on. It's time to go.'' He heard a man's voice say. _Go where? _He thought. Panic began to rise in his chest. He couldn't move or speak. ''I don't want to leave him.'' The girl responded, a hint of stubbornness coming through in her words. Her voice sounded somewhat familiar but no image of her face would form in his mind. Like a memory from when he was a child that he couldn't quite grasp. Wasn't this a memory, though? How could he possibly try to remember a memory in a memory? Nothing of it made sense.

''You know why we're doing this.'' The man seemed to hesitate for a moment. Thomas could feel his eyes on him, knew somehow that the man wasn't sure how much he could say with him in the room. He heard some shuffling of feet before the man finally spoke up again. ''Five more minutes, then we're leaving. If you're not outside this door by the time your five minutes are over, I'll be coming back inside to take you away myself.'' The man was once again silent. His voice was softer when he opened his mouth again. He almost sounded . . . pitiful. ''Don't make this harder for yourself than it already is.'' The door closed again and the room went quiet. Though, he could sense the girl's presence as she stood beside his bed, or whatever he was lying upon.

A small, warm hand took his, giving a reassuring squeeze. Her skin felt soft against his calloused one. Her holding his hand felt right in a way. Almost natural. She was so close that he could smell her. He had no idea what the scent was, but it put him at ease - comforted him - and if he could have, he would've smiled. ''I'm sorry it didn't work.'' Her voice finally broke the silence. ''But I will find you. Things will be like they used to, I promise.'' She said and leaned in to press a subtle kiss to his forehead, her long hair tickling his cheek. ''See you soon.'' She whispered. Hearing the sadness in her voice, he wanted so badly to open his eyes. To take the girl that he knew but also didn't know in his arms and comfort her in a way that he knew only he could. To tell her that everything was going to be okay. But his mind began to get clouded. He was being pulled away from the light, away from her.

_Teresa_

That was the last word to appear in his mind, and he mentally held on to the name as darkness swallowed him whole.


	2. Chapter 1

**Disclaimer: **I do not own The Maze Runner or any of its characters. The plot, however, is mine.

* * *

Chapter 1

* * *

Thomas' head was pounding, and not just pounding like a normal headache. His head felt as if someone had smashed his skull with a mallet. He laid as still as he possibly could, gathering some of the energy he had left before lifting his upper torso of the bed with a groan. His brows creased, which only seemed to increase the pain and caused him to release yet another groan. ''Christ..'' He grumbled. His lids slowly fluttered open and Thomas squinted against the bright lights.

After his eyes had gotten somewhat accustomed, he carefully stretched either limb. He was sore, but other than that, nothing seemed damaged. Thomas scooted over to the edge of the bed and slipped out. A bit unsteadily, he staggered backwards to get a better view of the room. The walls were white. It almost looked therapeutic. But not only the walls were white; also the floor, the ceiling. Even the bed sheets. It reminded Thomas of a hospital, even though he didn't recall ever actually going to one. From what he could remember of the previous night - at least, he thought it was the previous night. He wasn't entirely sure how much time had passed - he wasn't in the same room anymore. They'd moved him. _Why though?_ He thought. _And who are they?__  
_

He stumbled towards the door and tried to open it. It wasn't locked, which confused him greatly. Thomas took a peek outside to see if anyone was there. When he figured it was safe to go, he quietly shuffled out of his room. It wasn't until then that he wondered what he was wearing, and he glanced down. He was wearing a white shirt with the sleeves rolled up to his elbows, dark-blue jeans and a pair of black Chuck Taylors. Though, he didn't know whether it was what he liked to wear or something they'd picked out for him.

Deciding not to dwell on it for too long, Thomas hesitantly began wandering around the hallways, not wanting to get lost and unable to find his way back to his room. When he reached the end of the hall, he heard hushed murmurs coming out of the room on his left. He held his breath and pressed his ear to the door, straining to hear what the voices were saying.

...

''What are we waiting for? It's been almost a week since Subject A2 was supposed to be sent into The Maze. _The girl has to go.__**''**_

A.D. Janson frowned at the young doctor before him. He'd insisted to wait with sending Subject A1 into The Maze, simply because she refused to be operated as long as she couldn't be sure of the recovery of Subject A2. She would resist in any way possible, and he couldn't risk having to keep her out of The Maze, too. Too much had already changed. Even now he wasn't sure if the experiment was going to work properly, and if so, he'd have to rely completely on Group B. ''How about we administer an anesthetic.'' Someone else spoke up, seeming to be determined to get subject A1 into The Maze as soon as possible. ''She'll lose consciousness. We can make sure to use a high enough dosage so she won't wake up until she's in the metal box. Everything should go according to plan.''

Janson let out a somewhat exasperated sigh and closed his eyes, raking his hands through his hair before finally muttering. ''Alright, alright. Go get the girl. I'll perform the operation myself. Just to be safe.'' The people around him nodded once before lifting from their chairs and moving towards the door.

...

It took Thomas a while before he realized the people inside the room had to leave through the door he was sitting in front of. Quickly scrambling up, he hurriedly made his way back to the room he'd woken up in, closed the door and lay down, allowing his eyes to close and pretending to be asleep. What he'd just heard had him more confused than ever. Too confused to even notice that he wasn't alone in the room.

''Thomas?'' A small voice filled with uncertainty spoke up. He recognized the voice and sat upright, his head twisting the way the sound had come from. The instant his eyes took in the figure standing before him, something in his mind clicked in place. She was the girl who had been with him last time he'd woken up. She'd been the girl who's voice he had recognized but who's face he couldn't picture. She was-

''I'm Teresa..'' She said, seeming to be unsure of how to introduce herself. She averted her eyes from his and looked down, nervously fumbling with the hem of her shirt. ''I know.'' Thomas replied in a relieved tone. Finally someone he remembered. He smiled, trying to put her somewhat at ease. Though, his words seemed to have the exact opposite effect.

Teresa's head snapped up, a look of confusion clearly evident upon her features. ''What do you mean, _you know?_'' She stumbled backwards a bit, as if what he'd just said completely changed the situation between the two of them. Though, clearly Thomas was the one with the least knowledge of the matter.

''I just recognized your voice is all.'' He replied a bit defensively, somewhat offended because she seemed scared - of him, out of all people - but mostly confused. ''You were with me a while back. You promised me everything would be okay and that you'd find me.'' He paused for a moment, hoping he'd convinced her that there was no reason to be afraid of him. _''You found me.''_ He repeated, sounding more sure of himself this time.

''But they said. . .your brain. They said..'' Teresa was still confused but at least she didn't look afraid of him anymore and that'd have to do for now. He had to tell her what he'd overheard the doctors say. ''Listen, I think we need to talk about something. It's really important and I don't think I was supposed to hear it but-'' Thomas was cut off in the middle of his sentence when her hand suddenly clamped over his mouth. She held a finger before her lips, indicating for him to keep quiet ''Listen..'' She whispered.

At first, Thomas couldn't hear a thing but the thumping of his own heart in his ribcage due to Teresa being so close, but then he heard it too. Footsteps in the distance, and they seemed to be heading their way. Teresa carefully removed her hand and mouthed, 'Lie down and pretend to sleep.' to him before scooting towards the corner of the room and sitting down.

Thomas blindly trusted her and did as he was told, lying down on the bed and closing his eyes. It wasn't long after that or the door opened and a bunch of people entered the room. ''There you are.'' A voice spoke up. Thomas had to fight the urge to open his eyes, knowing deep down they weren't talking to him. He recognized the voice of the man from earlier. ''You have to come with us.''

''No.'' She said persistently, and he could hear her move away. He opened his eyes at a slight so he could see what was going on. Three men and a woman were standing in the room and had Teresa cornered. No one seemed to be paying attention to him. ''I'm not going anywhere.'' She said, her lips pursed in disapproval. One of the male doctors looked over to the female one and nodded, then everything happened at once. Two of the male doctors grabbed Teresa by the arms while the other moved forward to grab her legs. Though, not being quick enough Teresa managed to deliver a swift kick between his legs, causing the man to crumple to the floor in agony, almost causing Thomas to laugh out loud.

''That's enough.'' Thomas heard the female doctor mutter. She too, seemed amused. She nudged the doctor lying on the floor aside and forced a cloth over Teresa's mouth. Her eyes grew wide with panic and she struggled to get away, though her attempts got weaker and weaker until her eyes closed and she hang limp in one of the male doctor's arms.

''Let's get her out of here.'' Someone said and Thomas shut his eyes again, not wanting them to know he'd seen the entire thing. There was some shuffling of feet and the sound of a door closing.

Thomas was once again alone.


	3. Chapter 2

**Disclaimer:** I do not own The Maze Runner or any of its characters. The plot, however, is mine.

* * *

Chapter 2

* * *

Thomas didn't know how long he'd been wandering around in his room after he'd woken up. A few minutes, half an hour? A couple hours, maybe? He had no idea. Maybe time wasn't passing at all and he was in some other strange universe. No one had come in to check up on him since they'd taken Teresa - at least, not while he was awake - and he was just starting to wonder if maybe everyone had just disappeared when he heard the faint noise of footsteps. Someone was hurriedly making his way through the hall. Figuring said person was heading toward his room, he laid back down on his cot, folding his arms neatly over his chest whilst allowing his eyes to close, trying to maintain a steady breathing.

The footsteps stopped before his door and everything went quiet again. The hinges made a squeaking sound as the door opened just a tad, a small beam of light shining into the room from the lit hallway and then it disappeared. Thomas released the breath he didn't realize he was holding. Before he'd gone to sleep his headache had been almost gone, but now it was back at full force, demanding all his attention. Maybe it had something to do with the dream he'd had? What if it wasn't a dream after all. What if it was. . .a memory?

* * *

_Thomas held his stomach, joyful laughter rumbling from within the depths of his chest as he watched Teresa. Her mouth hung slightly open due to the indignant gasp that had just left her lips, ice cream dripping from her forehead all the way down to her chin, the sticky substance quickly beginning to form a puddle on the mahogany table._

_''What the-'' she started saying, furiously trying to wipe her face clean which only caused Thomas to laugh harder, resulting in him losing his balance and falling off the chair. Teresa shifted and bent to peek underneath the table, opening her mouth to ask if he was alright but she once again stopped herself when she found him red-faced and rolling over the floor. ''Whatever,'' she grumbled beneath her breath and pushed her chair away from the table. She stood up, arms crossing in front of her chest in defense._

_As she started to walk away, she got distracted by the full-length mirror on the wall, and she couldn't help but smile. She did look ridiculous. A string of hair clung to her face, caught in the trail of molten ice cream. Teresa shook her head at her reflection and tucked the strand of hair behind her ear. She'd take a shower later._

_A strong pair of arms encircled her waist from behind and she sighed, instantly giving in to Thomas' warmth and leaning her back against his chest. She closed her eyes, enjoying the way her body naturally adjusted to his. ''You know I was just kidding, right?'' he muttered and nuzzled his face in the crook of her neck, causing her to shift against him._

_''Yeah, yeah..'' she replied and grinned before burying her still with ice covered features in his hair. He groaned in disapproval, but she could see the amusement sparkle in his eyes when he pulled back. She reached up on her tiptoes and allowed her lips to brush over his jaw before murmuring, ''Go wash yourself.'' She lowered herself back on her feet. He was taller despite the fact that she was older. Not that their age differed that much. She was 18 and he was 17, so technically it was only a few months._

_''Mm..'' Thomas hummed, pressing a brief kiss to her forehead. He moved towards the door, but before he had the chance to open it A.D. Janson waltzed in. He took a moment to observe the scenery before him, and after a short while he simply shook his head, deciding not to comment on the way they looked. Thomas glanced over at Teresa and she was nervously shifting from one foot on the other. The fact that the doctor had shown up was bad news. Thomas drew in a deep breath and straightened up, his jaw set as he muttered through clenched teeth. ''It's time, isn't it?''_

_Janson nodded, repeating the same words Thomas had just said. ''It's time.''_

* * *

That's when Thomas had woken up. He still hadn't figured out what 'It's time.' had meant, and it was driving him absolutely crazy. The pounding in his head wasn't exactly what he would call helpful, and he'd eventually ended up pacing the room. Thomas was about to move off the bed when he heard someone whisper outside his room. ''Come on, hurry.'' Thomas' brows furrowed in confusion. Was the voice talking to him? Did they know he was awake? He was about to ask where to, but the voice spoke up again. ''The anesthetic can wear of any minute now.'' He pursed his lips into a thin line. Right. Of course they didn't mean him.

Without making any noise, he shuffled towards the door, leaning in close and hoping he would be able to pick up anything else.

...

''Alright, alright. I just want to make sure the entire process went well this time.'' A.D. Janson grumbled beneath his breath. The other doctor was being incredibly inpatient and it was starting to get on his nerves. He couldn't risk another mistake. It would mean the end for him and his job at WICKED. Subject A1 and A2 both not being able to participate in the experiment would mean it would be a complete disaster. Eleven years of research gone to waste. At least they had somewhat of a chance with one of them inside the Maze. ''Oh for God's sake, get on with it already.'' The doctor hissed, the tension clearly sounding through in his voice.

Janson decided not to reply and simply did a few more check ups before bobbing his head in a small, rather relieved nod. ''She's good to go.'' A.D. Jason removed his gloves and tossed them into the bin next to the operation table and watched as two muscled men lifted subject A1 off the operating table, moving her onto a transportable one before pushing her out of the room. This was it. The moment they'd all been waiting for. As soon as subject A1 arrived into the Maze, everything - the rules they'd made, the life they'd build up - everything they'd all been starting to see as normal was going to change.

There was this tiny voice in the back of Janson's head that told him this was a bad idea. Everyone knew the Gladers were going to turn themselves against subject A1. Not only because their lives would turn upside down as soon as she showed up, but also because she was a girl. And not just a girl. The only girl, to be more specific. The original plan had been to put subject A2 into the Maze, followed by A1. Being reunited so quickly after just having their memories swiped would leave both subjects without any real memories, but with the strong feeling of recognition. The urge to bond. Subject A2 would take subject A1's side, and together they would get the whole escape process going. The entire theory was now useless.

Janson sighed and followed the men to the control room with the metal box they used to send their subjects into the Maze. This was the last time it was going to go up, and it wasn't something he was going to miss. This was it. The moment they'd all been waiting for. The beginning of the end of the first experiment. Either it was going to work, or things were going to go terribly wrong.

They lifted subject A1 up and carefully lowered her body on the bottom of the box. One of the doctors reached into the pocket of his lab coat and retrieved a small note, placing it in subject A1's palm and folding her fingers around it. ''She's the last one. Ever.'' he murmured before taking a step back when the red light above the elevator shaft began to flash, indicating that the doors were going to close. Everyone gathered in a half-circle, watching as the doors closed when suddenly something hard connected with Janson's side, the impact of the collision sending him flying into the doctor beside him and causing both of them to fall to the floor. In a reflex, everyone else turned to them, reaching out to help them up.

He was standing just in time to see a brown-haired boy disappear into the metal box right before it went up.


End file.
